ds006072 dataset cifti parcelation issue

[Giannis Fotis]

Hi everyone,

I am working on this dataset for my master's thesis, and I am trying to apply a parcelation on the cifti files in the NON_BIDS/ciftis/ folder using the hcp library in python. 

For some reason, it seems that all the parcelation maps have 91282 grayordinates, while the ciftis in my dataset have 91206 . Here's the exact error I'm getting:
IndexError: boolean index did not match indexed array along dimension 1; dimension is 91206 but corresponding boolean dimension is 91282

I havent managed to figure this out for a couple of days now... Can anyone help? Thanks!

Giannis

[Tim Coalson]

You can run wb_command -file-information -no-map-info on your cifti files and see how many indices are being used in each structure.  The standard 91k grayordinate space is 91282, and looks like this:

$ wb_command -file-information -no-map-info global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii

<SNIP>

Number of Rows:                 91282
Number of Columns:              1
Volume Dim[0]:                  91
Volume Dim[1]:                  109
Volume Dim[2]:                  91
Palette Type:                   Map (Unique for each map)
CIFTI Dim[0]:                   1
CIFTI Dim[1]:                   91282
ALONG_ROW map type:             SCALARS
ALONG_COLUMN map type:          BRAIN_MODELS
    Has Volume Data:            true
    Volume Dims:                91,109,91
    Volume Space:               -2,0,0,90;0,2,0,-126;0,0,2,-72
    CortexLeft:                 29696 out of 32492 vertices
    CortexRight:                29716 out of 32492 vertices
    AccumbensLeft:              135 voxels
    AccumbensRight:             140 voxels
    AmygdalaLeft:               315 voxels
    AmygdalaRight:              332 voxels
    BrainStem:                  3472 voxels
    CaudateLeft:                728 voxels
    CaudateRight:               755 voxels
    CerebellumLeft:             8709 voxels
    CerebellumRight:            9144 voxels
    DiencephalonVentralLeft:    706 voxels
    DiencephalonVentralRight:   712 voxels
    HippocampusLeft:            764 voxels
    HippocampusRight:           795 voxels
    PallidumLeft:               297 voxels
    PallidumRight:              260 voxels
    PutamenLeft:                1060 voxels
    PutamenRight:               1010 voxels
    ThalamusLeft:               1288 voxels
    ThalamusRight:              1248 voxels

I have never seen 91206 before, but maybe someone intersected the medial wall ROIs?  nibabel should expose the information of exactly what vertices/voxels are used in the embedded XML extension, but I'm not familiar with its API.  There is also wb_command -cifti-export-dense-mapping if you want to inspect it via text files.

Tim

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[Giannis Fotis]

Dear Tim,

Thank you for the tip! Here's what I get when I run this command on my time series data:

Type:                           CIFTI - Dense Data Series
Structure:                      CortexLeft CortexRight
Metadata Start:                 -----------

[...]

Data Size:                      543.59 Megabytes
Maps to Surface:                true
Maps to Volume:                 true
Maps with LabelTable:           false
Maps with Palette:              true
All Map Palettes Equal:         true
Map Interval Units:             NIFTI_UNITS_SEC
Map Interval Start:             0.000
Map Interval Step:              1.761
Number of Rows:                 91206
Number of Columns:              1490

Volume Dim[0]:                  91
Volume Dim[1]:                  109
Volume Dim[2]:                  91

Palette Type:                   File (One for all maps)
CIFTI Dim[0]:                   1490
CIFTI Dim[1]:                   91206
ALONG_ROW map type:             SERIES
    Start:                      0.000
    Step:                       1.761
    Units:                      Seconds

ALONG_COLUMN map type:          BRAIN_MODELS
    Has Volume Data:            true
    Volume Dims:                91,109,91

    Volume Space:               2,0,0,-90;0,2,0,-126;0,0,2,-72

    CortexLeft:                 29696 out of 32492 vertices
    CortexRight:                29716 out of 32492 vertices

    AccumbensLeft:              84 voxels
    AccumbensRight:             111 voxels
    AmygdalaLeft:               256 voxels
    AmygdalaRight:              291 voxels
    BrainStem:                  3581 voxels
    CaudateLeft:                621 voxels
    CaudateRight:               618 voxels
    CerebellumLeft:             9316 voxels
    CerebellumRight:            9260 voxels
    DiencephalonVentralLeft:    734 voxels
    DiencephalonVentralRight:   724 voxels
    HippocampusLeft:            705 voxels
    HippocampusRight:           688 voxels
    PallidumLeft:               335 voxels
    PallidumRight:              332 voxels
    PutamenLeft:                772 voxels
    PutamenRight:               805 voxels
    ThalamusLeft:               1312 voxels
    ThalamusRight:              1249 voxels

Someone suggested to me that I "use wb_command -cifti-create-dense-from-template 1 to resample one to the other".  Does that sound right to you? And should I resample me time series data or the parcelation maps? Many thanks!

Best,
Giannis

[Glasser, Matthew]

Your subcortical voxels do not match ours.  How was this file generated?

    ThalamusRight:              1248 voxels

Matt.

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[Giannis Fotis]

Dear Matt,

These files are the already preprocessed fMRI recordings in this openneuro.org dataset, found in the NON_BIDS/ciftis/ folder. They are were published together with the paper: 
Siegel, J.S., Subramanian, S., Perry, D. et al. Psilocybin desynchronizes the human brain. Nature 632, 131–138 (2024). https://doi.org/10.1038/s41586-024-07624-5 

This is pretty much the first time I work on fMRI data, so I probably can't say much more that would be accurate, and thats why I'm refering you to the source material... I hope this is useful. If there is anything specific I can search for you I'd be more than glad to. Thank you for your time.

Best,

Giannis

[Tim Coalson]

Given that you have more brainstem and cerebellum voxels, and fewer voxels in many other cortical structures, I wonder whether the subcortical data in your file is actually in MNI space or not.  If it isn't, you will need to use a transform in -cifti-resample in order to preserve as much of the data as possible (-cifti-resample doesn't allow data to cross between subcortical structures, so if they aren't aligned, it will clip off data).

-cifti-create-dense-from-template would be reasonable when the subcortical definitions agree.  Here they don't, so -cifti-resample is the better choice (particularly because of its -volume-predilate option).  I also notice that your voxel data uses LPI order (the X spacing is positive), while the standard 91k grayordinates use RPI order (negative X spacing), so -cifti-create-dense-from-template would reject the file anyway.

Tim